tbuckley/cabot-search huggingface dataset:
Abstract 1851: Mechanisms underlying focused ultrasound-induced immunogenicity in melanoma
Authors: Sandra Pelka, Sanmay Bandyopadhyay, Sanjay Pandey, Chandan Guha, Fernando Macian
Journal: Cancer Research (2023)

Abstract Advanced melanoma is an aggressive skin cancer characterized by low survival rates. The generation of a robust anti-tumor response relies on dendritic cells (DCs) to process tumor antigens, migrate to draining lymph nodes, and activate T-cells. Within the tumor microenvironment, immunosuppressive factors impede DC differentiation and activation, and the subsequent immature DC phenotype is a major mechanism underlying the ineffective T-cell response in melanoma patients. We have shown that low-intensity focused ultrasound (LOFU), a novel therapy that delivers mechanical and thermal stresses locally at the tumor site, may enhance DC function in a B16 murine melanoma model. We hypothesize that LOFU enhances the dendritic cell-mediated anti-tumor response by inducing changes in tumor cell and dendritic cell autophagy and increasing pro-immunogenic factors in the TME. Autophagy is a lysosome-dependent process of cellular content degradation that has previously been implicated in the regulation of multivesicular body formation/degradation, and thus in the secretion of extracellular vesicles. Autophagy may subsequently modify the cargo of tumor-derived extracellular vesicles, such as exosomes, in a pro-immunogenic manner. We have found that LOFU treatment is associated with an increase in autophagic flux in melanoma cells and have identified at least 82 proteins within melanoma-derived extracellular vesicles that are significantly enriched or reduced with LOFU treatment, with enriched proteins partaking in essential processes including antigen processing, intracellular trafficking, and cellular metabolism. DCs pulsed with vesicles from LOFU-treated melanoma cells have shown enhanced activation of both CD4+ and CD8+ T-cell activation, suggesting that the LOFU-induced increase in tumor cell autophagy and modification of vesicular cargo may promote a DC-activated anti-tumor antigen activation response. Characterization of other mechanisms by which LOFU may enhance DC function, such as direct changes in DC autophagy, is critical to elucidate DC-mediated pathways involved in the anti-tumor response. Further understanding of DC involvement in the anti-tumor response will provide novel targets for the development of immunotherapies to improve survival and quality of life in advanced melanoma patients. Citation Format: Sandra Pelka, Sanmay Bandyopadhyay, Sanjay Pandey, Chandan Guha, Fernando Macian. Mechanisms underlying focused ultrasound-induced immunogenicity in melanoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1851.
Abstract 1051: Liquid biopsy in the detection of genetic biomarkers in gastrointestinal cancer
Authors: Bianca Gomes-Fernandes, Juliana Garcia Carneiro, Rodrigo Gomes da Silva, Luiz de Marco, Luciana Bastos-Rodrigues
Journal: Cancer Research (2023)

Abstract Colorectal cancer (CRC) is one of the leading causes of morbidity and mortality worldwide. Detection prior to metastasis and appropriate therapeutic application lead to greater patient survival and quality of life. However, the diagnosis and postoperative surveillance are surrounded by limitations. Genetic biomarkers are influential factors that contribute to favorable clinical outcomes. To better understand the molecular basis associated with CRC, we investigated KRAS, NRAS, BRAF, EGFR and TP53 genes in the DNA of tumor and healthy cells using Sanger sequencing. The most frequent alteration, present only in the tumor DNA (somatic), was used to investigate, by Digital PCR (ddPCR), the detection and analysis of circulating tumor DNA (ctDNA) in the plasma. Altogether, 42 subjects made up the study, most of them male (59.5%), with a mean age of 63 years and tumors located in the right colon (21.4%). transversal (2.4%), left (4.8%), sigmoid (33.3%) and straight (38.1%). Germline and somatic allelic variants were found in the KRAS, EGFR and TP53 genes. The most frequent somatic alteration in the study was rs121913529, which showed an association with alcohol consumption (p = 0.002). Patients with a somatic mutation in TP53 are ten times more likely to die, compared with the chance of those without a mutation in this gene (OR 11.2; 95% CI 1.25 - 245). The applicability of these somatic changes in the liquid biopsy technique was demonstrated by ddPCR. Therefore, the results obtained expand the understanding of the molecular basis of CRC and present an optimization of the liquid biopsy, timely for clinical practice. Citation Format: Bianca Gomes-Fernandes, Juliana Garcia Carneiro, Rodrigo Gomes da Silva, Luiz de Marco, Luciana Bastos-Rodrigues. Liquid biopsy in the detection of genetic biomarkers in gastrointestinal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1051.
Abstract 3338: Targeted serum metabolomics for noninvasive detection of colorectal neoplasia
Authors: Liam W. Fitzgerald, Dennis J. Orton, Karen A. Kopciuk, Hans J. Vogel, Robert J. Hilsden, Oliver F. Bathe
Journal: Cancer Research (2023)

Abstract Background: Using a shotgun metabolomics approach, we have previously reported distinct features in the circulating metabolome of patients with colorectal cancer (CRC) and adenoma. A clinically useful metabolomic assay requires a targeted approach that detects CRC with high sensitivity, and which also detects pre-malignant precursor lesions. Our objective was to identify a metabolomic signature for CRC, adenomatous polyps (AP), and sessile serrated adenomas (SSA), using a targeted approach. Methods: Serum from patients with all stages of CRC (N=86), AP (N=48), SSA (N=46), as well as age- and sex-matched disease-free controls (DFC; N=120) were analyzed using a targeted metabolomic assay (Biocrates MxP® Quant 500). The assay was performed on liquid chromatography-tandem mass spectrometry (LC-MS/MS), quantifying 630 metabolites across 26 biochemical classes. Orthogonal partial least squares-discriminant analysis (OPLS-DA) was used to identify metabolite patterns distinguishing each neoplastic condition relative to DFCs. A small validation cohort (N=78) was additionally analyzed to test our meta-biomarkers. Results: In comparisons with DFCs, statistically significant OPLS-DA models were constructed for all three neoplastic conditions. The OPLS-DA models for CRC, AP, and SSA consisted of 39, 14, and 22 metabolites, respectively, with the most frequently represented biochemical classes being triglycerides, phosphatidylcholines, bile acids, and acylcarnitines. Based on 7-fold internal cross validation, receiver operating characteristic (ROC) analysis demonstrated an area under the curve (AUC) of 0.85, 0.89, and 0.82 for CRC, AP, and SSA, respectively. When applied to the independent validation cohort, the sensitivity and specificity of each model were: 87.0% and 87.0% for CRC; 53.3% and 93.3% for AP; and 78.6% and 57.1% for SSA. Conclusion: Metabolomic meta-biomarkers for CRC and its precursors demonstrated excellent performance based on internal validation. Importantly, these lesions were each detected with superior sensitivity compared to readily available stool-tests. A large external validation study in progress will be used to confirm these findings. Citation Format: Liam W. Fitzgerald, Dennis J. Orton, Karen A. Kopciuk, Hans J. Vogel, Robert J. Hilsden, Oliver F. Bathe. Targeted serum metabolomics for noninvasive detection of colorectal neoplasia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3338.
Abstract 6287: Selective CBP degradation shows superior potency and differentiated biological activity compared to small molecule inhibitors
Authors: Laura La Bonte, Darshan Sappal
Journal: Cancer Research (2023)

Abstract CREB binding protein (CBP) and E1A binding protein (p300) are paralog histone acetyltransferases involved in many cellular processes via their activity as transcription factor co-activators. Dysregulation of one or both proteins has been implicated in a variety of cancers, and functional genomic screens have exhibited a bidirectional synthetic lethal relationship between the two genes in many cancer indications. Due to the high homology between CBP and p300, identification of selective chemical matter that specifically and directly targets CBP has proven challenging. Small molecule inhibitors (SMIs) targeting the HAT or bromodomain of CBP/p300 have been developed, however these agents are not selective for either paralog and inhibit both proteins equally, potentially limiting their clinical application. Herein, we describe the biological activity of selective, potent CBP degraders and show differentiation from SMIs. Citation Format: Laura La Bonte, Darshan Sappal. Selective CBP degradation shows superior potency and differentiated biological activity compared to small molecule inhibitors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6287.
Abstract 2302: Detection of tumor-associated methylation and mutation signatures for early colorectal cancer diagnosis
Authors: Pushpinder Bains, Mikhail Kulak, Zhen Cui, Alisha Babu, Stella Tran, Bongyong Lee, Aiguo Zhang, Michael Sha
Journal: Cancer Research (2023)

Abstract Introduction: The ability to identify epigenetic signatures, together with genetic alterations, has expanded the translational utility of genomic sequencing in clinical settings. Epigenetic changes may appear at very early stages before diagnosis. Thus, they could be used as epigenetic biomarkers for early detection or risk of cancer development. Circulating cell-free DNA (cfDNA) profiling has emerged as a promising biomarker for cancer diagnosis and prognosis. Herein, we developed targeted next-generation sequencing (NGS) based assays for assessing multiple DNA methylated and mutated regions in both low-quantity (plasma cfDNA) and low-quality formalin-fixed paraffin-embedded (FFPE) tissue for colorectal cancer (CRC) detection. Methods: For the OptiSeqTM CRC methylation panel, we assessed the methylation status of CpG dinucleotides in 42 genes. With this panel, we profiled 6 CRC samples (matching cfDNA and FFPE), 2 primary colon tumors with adjacent normal, and 6 advanced adenomas (AA) FFPE tissue DNA. For healthy individuals, we profiled 12 normal colon FFPE samples and 31 plasma cfDNA (26 matching buffy coat DNA samples). For the OptiSeqTM CRC mutation panel, the mutation status was assessed in 43 genes. Here, we profiled 6 CRC samples (matching cfDNA and FFPE), 19 CRC plasma cfDNA, 4 AA FFPE and 42 healthy individuals’ plasma cfDNA (26 matching buffy coat DNA samples). The analytical and clinical performance for both panels (separately and combined) were calculated using advanced adenoma (AA), CRC, and cancer-free individuals. Results: For CRC cfDNA samples, clinical samples testing showed that the methylation panel had a sensitivity of 50% (95% CI: 13.9-86.0) and specificity of 100% (95% CI: 86.2-100) while the mutation panel yielded the sensitivity 88% (95% CI: 67.7-96.8) and specificity 100% (95% CI: 89.5-100). Combining the mutation panel with the methylation panel, the sensitivity increased to 100% (95% CI: 51.6-100) and specificity to 100% (95% CI: 65.1-93.3). For AA FFPE samples, the methylation panel analysis yielded a sensitivity of 100% (95% CI: 39.5-100.0) and a specificity of 100% (95% CI: 67.8-100). Conclusion: We have developed and validated the targeted NGS-based panels to detect clinically relevant mutation and methylation patterns and demonstrate its potential as a highly sensitive assay for early CRC diagnosis. Citation Format: Pushpinder Bains, Mikhail Kulak, Zhen Cui, Alisha Babu, Stella Tran, Bongyong Lee, Aiguo Zhang, Michael Sha. Detection of tumor-associated methylation and mutation signatures for early colorectal cancer diagnosis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 2302.
Abstract 546: Targeting <i>BRAF</i> mutations in head and neck cancer
Authors: Chun Ho Law, Franky Leung Chan, Vivian Wai Yan Lui
Journal: Cancer Research (2023)

Abstract The mitogen-activating protein kinase (MAPK) pathway [RAS/RAF/MEK/MAPK] is a well-known mitogenic pathway essential for regulation of cell proliferation, survival, differentiation, invasion, and apoptosis, etc. In normal cells, upon the binding of external stimuli, activated Ras relays the signals through a RAF-MEK-ERK (MAPKKK-MAPKK-MAPK) phosphorylation cascade, leading to MAPK pathway activation. On the other hand, in cancer cells, aberrations or mutations of the pathway components usually could lead to constitutive activation of the pathway, resulting in dysregulation of these cellular processes. Notably, mutations of MAPK pathway components are found in 18% of head and neck cancer (HNC). Among these, mutations of the serine/threonine-protein kinase B-Raf (BRAF gene) account for about 1.8% of HNC (based on TCGA-HNSCC cohort, USA). Serving as one of the key kinase members of the MAPK pathway, BRAF is considered as a precision drug target in various cancer types, including melanoma, thyroid cancer, and non-small cell lung cancer (NSCLC). While the significance of BRAF mutations remains underexplored in HNC, exceptionally favorable responses to BRAF and MEK inhibition had been reported in HNC patients carrying BRAF-mutations. Based on this, we hypothesize that BRAF mutations may confer drug sensitivity and serve as a predictive biomarker for personalized therapy in HNC. Here, we demonstrated that ectopic overexpression of mutated BRAF resulted in MAPK pathway activation in HNC cell models. We also showed that ectopic BRAFV600E could promote the in vitro growth of head and neck cancer cells in both 2D and 3D culture conditions as well as enhance anoikis resistance, which is a prerequisite for metastasis. Further preliminary results showed that the mutated BRAFV600E mutant could promote the invasiveness of HNC cells. In summary, our findings support that targeting the BRAF mutants could be a potential therapeutic approach or precision treatment for HNC. (This study was supported by the Research Impact Fund (R4015-19F in the period of 6/29/2020-9/7/2021) from the Research Grants Council, University Grants Committee, Hong Kong SAR.) Citation Format: Chun Ho Law, Franky Leung Chan, Vivian Wai Yan Lui. Targeting BRAF mutations in head and neck cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 546.
Abstract 3607: RNA-binding proteins are essential for EGF-induced fibronectin expression and metastasis of head and neck squamous cell carcinoma
Authors: Ting-Wei Chang, Wen-Chang Chang, Ben-Kuen Chen
Journal: Cancer Research (2023)

Abstract There is a higher expression level of epidermal growth factor receptor (EGFR) in up to 90% of advanced head and neck squamous cell carcinoma (HNSCC) tissue than in normal surrounding tissues. However, the precise mechanism involved in modulating EGF-associated metastasis in HNSCC remains unclear. In this study, we reveal that the concurrent expression of EGFR and fibronectin (FN1) was highly associated with the stages of HNSCC progression. EGF-induced fibronectin/integrin axis enhanced tumor-endothelial cell interaction and increased endothelial permeability, conferred HNSCC cell metastasis. Mechanistically, we found that ERK and NF-κB pathway activation was essential for EGF-induced fibronectin expression. In addition, EGF-enhanced mRNA stability of fibronectin occurred through the 5’ untranslated region (5’-UTR) of the gene and was mediated by nucleolin (NCL) and hnRNPA2/B1, which were also involved in the regulation of epithelial-mesenchymal transition gene expression. Intriguingly, the in vivo study showed that depletion of NCL, hnRNPA2/B1, and inhibition of the fibronectin/integrin axis significantly inhibited EGF-promoted HNSCC metastasis in the lung. Our data suggests that the nucleolin/hnRNPA2/B1-regulated fibronectin is essential for EGF-induced tumor-endothelial cell interactions to enhance HNSCC cell metastasis. Citation Format: Ting-Wei Chang, Wen-Chang Chang, Ben-Kuen Chen. RNA-binding proteins are essential for EGF-induced fibronectin expression and metastasis of head and neck squamous cell carcinoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 3607.
Abstract 6257: Developing HDAC inhibitors as immunomodulators
Authors: Sean Colligan, Li Shen, Christopher Rupert, Jonathan Bard, Roberto Pili
Journal: Cancer Research (2023)

Abstract Immune checkpoint inhibitors (ICIs) are standard of care for several solid tumor types, including renal cell carcinoma (RCC). However, the clinical success of these therapies is dampened by the fact that the majority of patients demonstrate either inherent resistance to treatment or develop secondary resistance following an initial response. One key mechanism of tumor-driven ICI resistance is the generation and recruitment of suppressive immune cell types, including regulatory T cells (Tregs) and myeloid-derived suppressor cells (MDSCs), which coordinate to suppress anti-tumor T cell responses. Thus, there is a critical need for the development of novel combination strategies aimed at mitigating the presence and function of suppressive immune cells to improve the efficacy of ICIs in the clinic. Our laboratory has previously demonstrated that histone deacetylase inhibition (HDACi) is associated with a decrease in both the number and function of tumor-infiltrating Tregs and MDSCs in the RENCA tumor model. Thus, the overall goal of these studies both preclinically and clinically is to investigate the impact of the immunomodulatory effects of HDACi in combination with ICI therapy, with the overall hypothesis that HDACi will improve the efficacy of anti-PD1 therapy in RCC. Our pre-clinical data support this hypothesis by demonstrating increased tumor control and survival in RENCA tumor-bearing mice when treated with a combination of anti-PD1 and HDACi compared to single agent therapy. These increases were also associated with an increase in the activation state of anti-tumor immune cells, as demonstrated by increased surface expression of MHC Class II molecules on macrophages and a decrease in phenotypically defined monocytic MDSCs. ATACseq and RNAseq data generated from combination-treated animals also outline a gene expression signature associated with both myeloid and T cell activation. Interestingly, our clinical studies also afforded us the opportunity to investigate potential biomarkers associated with responder status, which will allow us to better predict patient outcomes and administer therapies accordingly. Accumulating evidence from two independent clinical trials run by our group suggests that high levels of suppressive CD11b+HLA-DRlo MDSCs at baseline in the peripheral blood is associated with lack of clinical response to the combination of HDACi and ICI. Overall, these data support the rationale for the combination of ICI and HDACi in the clinic, and provide a potentially useful biomarker through which we can predict the success of combination therapy. Citation Format: Sean Colligan, Li Shen, Christopher Rupert, Jonathan Bard, Roberto Pili. Developing HDAC inhibitors as immunomodulators [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6257.
Abstract 6428: Targeting SMARCAL1 as a therapeutic strategy to enhance cGAS/STING signaling in gastric cancer
Authors: Po-Yen Hsu, Yu-Ming Chuang, Shu-Hui LIN, Yu-Ting Lee, Yin-Chen Chen, Enders K.W. Ng, Kun-Tu YEH, Alfred S.L. Cheng, Michael W.Y. Chan
Journal: Cancer Research (2023)

Abstract Gastric cancer is one of the leading causes of cancer death in Eastern Asia. Although immunotherapy, such as immune checkpoint blockade, is an emerging therapeutic strategy against gastric cancer, only a fraction of cancer patients show a therapeutic response. Therefore, developing a novel therapeutic strategy to turn a “cold” tumor into a “hot” tumor is considered a crucial issue in cancer treatment. By methylomic analysis, we found that SMARCAL1 is one of the STAT3 targets which might be regulated by STAT3-mediated promoter methylation. Moreover, an inverse correlation between SMARCAL1 promoter methylation and expression was observed in the TCGA online database and in our cell lines experiment. Bisulfite pyrosequencing also showed a significant hypomethylation of SMARCAL1 compared to gastritis and adjacent normal in our in-house cohort (gastritis n=15; IM n=13; cancer n=58). More importantly, SMARCAL1 knockdown showed increased sensitivity of gastric cancer cell lines to DNA-damaging agents and increase the expression of cGAS and its downstream target, IFNB1. Therefore, in this study, we propose SMARCAL1 as a therapeutic target for improving the efficiency of immunotherapy by enhancing the cGAS/STING signaling pathway. Citation Format: Po-Yen Hsu, Yu-Ming Chuang, Shu-Hui LIN, Yu-Ting Lee, Yin-Chen Chen, Enders K.W. Ng, Kun-Tu YEH, Alfred S.L. Cheng, Michael W.Y. Chan. Targeting SMARCAL1 as a therapeutic strategy to enhance cGAS/STING signaling in gastric cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6428.